Integrating sequence and array data to create an improved 1000 Genomes Project 
haplotype reference panel

Delaneau, O.; Marchini, J.; 1000 Genomes Project, Consortium; Lehrach, H.; Sudbrak, R.; Amstislavskiy, V. S.; Lienhard, M.; Mertes, F.; Sultan, M.; Timmermann, B.; Yaspo, M. L.; Herwig, R.

doi:10.1038/ncomms4934

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Integrating sequence and array data to create an improved 1000 Genomes Project haplotype reference panel

MPS-Authors

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Lehrach, H.
The 1000 Genomes Project Consortium;
Dept. of Vertebrate Genomics (Head: Hans Lehrach), Max Planck Institute for Molecular Genetics, Max Planck Society;

/persons/resource/persons73812

Lienhard, M.
The 1000 Genomes Project Consortium;
Bioinformatics (Ralf Herwig), Dept. of Vertebrate Genomics (Head: Hans Lehrach), Max Planck Institute for Molecular Genetics, Max Planck Society;

/persons/resource/persons50430

Mertes, F.
The 1000 Genomes Project Consortium;
Dept. of Vertebrate Genomics (Head: Hans Lehrach), Max Planck Institute for Molecular Genetics, Max Planck Society;

/persons/resource/persons50598

Timmermann, B.
The 1000 Genomes Project Consortium;
Sequencing (Head: Bernd Timmermann), Scientific Service (Head: Christoph Krukenkamp), Max Planck Institute for Molecular Genetics, Max Planck Society;

/persons/resource/persons50655

Yaspo, M. L.
The 1000 Genomes Project Consortium;
Gene Regulation and Systems Biology of Cancer (Marie-Laure Yaspo), Independent Junior Research Groups (OWL), Max Planck Institute for Molecular Genetics, Max Planck Society;

/persons/resource/persons50202

Herwig, R.
The 1000 Genomes Project Consortium;
Bioinformatics (Ralf Herwig), Dept. of Vertebrate Genomics (Head: Hans Lehrach), Max Planck Institute for Molecular Genetics, Max Planck Society;

External Resource

http://www.ncbi.nlm.nih.gov/pubmed/25653097
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引用

Delaneau, O., Marchini, J., 1000 Genomes Project, C., Lehrach, H., Sudbrak, R., Amstislavskiy, V. S., Lienhard, M., Mertes, F., Sultan, M., Timmermann, B., Yaspo, M. L., & Herwig, R. (2014). Integrating sequence and array data to create an improved 1000 Genomes Project haplotype reference panel. Nature Communications, 5:. doi:10.1038/ncomms4934.

引用: https://hdl.handle.net/11858/00-001M-0000-0025-B4D5-F

要旨

A major use of the 1000 Genomes Project (1000 GP) data is genotype imputation in genome-wide association studies (GWAS). Here we develop a method to estimate haplotypes from low-coverage sequencing data that can take advantage of single-nucleotide polymorphism (SNP) microarray genotypes on the same samples. First the SNP array data are phased to build a backbone (or 'scaffold') of haplotypes across each chromosome. We then phase the sequence data 'onto' this haplotype scaffold. This approach can take advantage of relatedness between sequenced and non-sequenced samples to improve accuracy. We use this method to create a new 1000 GP haplotype reference set for use by the human genetic community. Using a set of validation genotypes at SNP and bi-allelic indels we show that these haplotypes have lower genotype discordance and improved imputation performance into downstream GWAS samples, especially at low-frequency variants.